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libsbml.FbcModelPlugin Class Reference
Inheritance diagram for libsbml.FbcModelPlugin:
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Detailed Description

{fbc}

fbc Implementation of the 'fbc' package extention to the Model construct.

Public Member Functions

def addFluxBound
 
def addGeneAssociation
 
def addObjective
 
def clone
 
def createFluxBound
 
def createGeneAssociation
 
def createObjective
 
def getActiveObjective
 
def getActiveObjectiveId
 
def getElementByMetaId
 
def getElementBySId
 
def getElementNamespace
 
def getFluxBound
 
def getFluxBoundsForReaction
 
def getGeneAssociation
 
def getLevel
 
def getListOfAllElements
 
def getListOfFluxBounds
 
def getListOfGeneAssociations
 
def getListOfObjectives
 
def getNumFluxBounds
 
def getNumGeneAssociations
 
def getNumObjectives
 
def getObjective
 
def getPackageName
 
def getPackageVersion
 
def getParentSBMLObject
 
def getPrefix
 
def getSBMLDocument
 
def getURI
 
def getVersion
 
def removeFluxBound
 
def removeGeneAssociation
 
def removeObjective
 
def setActiveObjectiveId
 
def setElementNamespace
 
def unsetActiveObjectiveId
 

Member Function Documentation

def libsbml.FbcModelPlugin.addFluxBound (   self,
  args 
)

Python method signature(s):

addFluxBound(FbcModelPlugin self, FluxBound bound)   int

Adds a copy of the given FluxBound object to the list of FluxBounds.

Parameters
boundthe FluxBound object to be added to the list of FluxBounds.
Returns
integer value indicating success/failure of the operation. The possible return values are:
def libsbml.FbcModelPlugin.addGeneAssociation (   self,
  args 
)

Python method signature(s):

addGeneAssociation(FbcModelPlugin self, GeneAssociation association)   int

Adds a copy of the given GeneAssociation object to the list of GeneAssociations.

Parameters
associationthe GeneAssociation object to be added to the list of GeneAssociations.
Returns
integer value indicating success/failure of the operation. The possible return values are:
def libsbml.FbcModelPlugin.addObjective (   self,
  args 
)

Python method signature(s):

addObjective(FbcModelPlugin self, Objective bound)   int

Adds a copy of the given Objective object to the list of Objectives.

Parameters
boundthe Objective object to be added to the list of Objectives.
Returns
integer value indicating success/failure of the operation. The possible return values are:
def libsbml.FbcModelPlugin.clone (   self)

{fbc}

fbc Implementation of the 'fbc' package extention to the Model construct. Python method signature(s):

clone(FbcModelPlugin self)   FbcModelPlugin

Creates and returns a deep copy of this FbcModelPlugin object.

Returns
a (deep) copy of this FbcModelPlugin object
def libsbml.FbcModelPlugin.createFluxBound (   self)

Python method signature(s):

createFluxBound(FbcModelPlugin self)   FluxBound

Creates a new FluxBound object and adds it to the list of FluxBound objects and returns it.

Returns
a newly created FluxBound object
def libsbml.FbcModelPlugin.createGeneAssociation (   self)

Python method signature(s):

createGeneAssociation(FbcModelPlugin self)   GeneAssociation

Creates a new GeneAssociation object and adds it to the list of GeneAssociation objects and returns it.

Returns
a newly created GeneAssociation object
def libsbml.FbcModelPlugin.createObjective (   self)

Python method signature(s):

createObjective(FbcModelPlugin self)   Objective

Creates a new Objective object and adds it to the list of Objective objects and returns it.

Returns
a newly created Objective object
def libsbml.FbcModelPlugin.getActiveObjective (   self,
  args 
)

Python method signature(s):

getActiveObjective(FbcModelPlugin self)   Objective
getActiveObjective(FbcModelPlugin self)   Objective

Returns the current active objective.

def libsbml.FbcModelPlugin.getActiveObjectiveId (   self)

Python method signature(s):

getActiveObjectiveId(FbcModelPlugin self)   string

returns the id of the current active objective.

def libsbml.FbcModelPlugin.getElementByMetaId (   self,
  args 
)

Python method signature(s):

getElementByMetaId(FbcModelPlugin self, string metaid)   SBase

Returns the first child element it can find with the given metaid, or itself if it has the given metaid, or None if no such object is found.

Parameters
metaidstring representing the metaid of objects to find
Returns
a pointer to the SBase element with the given metaid.
def libsbml.FbcModelPlugin.getElementBySId (   self,
  args 
)

Python method signature(s):

getElementBySId(FbcModelPlugin self, string id)   SBase

Returns the first child element found that has the given id in the model-wide SId namespace, or None if no such object is found.

Parameters
idstring representing the id of objects to find
Returns
a pointer to the SBase element with the given id.
def libsbml.SBasePlugin.getElementNamespace (   self)
inherited

{core}

Representation of a plug-in object of SBML's package extension.

Additional attributes and/or elements of a package extension which are directly contained by some pre-defined element are contained/accessed by SBasePlugin class which is extended by package developers for each extension point. The extension point, which represents an element to be extended, is identified by a combination of a Package name and a typecode of the element, and is represented by SBaseExtensionPoint class.

For example, the layout extension defines <listOfLayouts> element which is directly contained in <model> element of the core package. In the layout package (provided as one of example packages in libSBML-5), the additional element for the model element is implemented as ListOfLayouts class (an SBase derived class) and the object is contained/accessed by a LayoutModelPlugin class (an SBasePlugin derived class).

SBasePlugin class defines basic virtual functions for reading/writing/checking additional attributes and/or top-level elements which should or must be overridden by subclasses like SBase class and its derived classes.

Package developers must implement an SBasePlugin exntended class for each element to be extended (e.g. SBMLDocument, Model, ...) in which additional attributes and/or top-level elements of the package extension are directly contained.

To implement reading/writing functions for attributes and/or top-level elements of the SBsaePlugin extended class, package developers should or must override the corresponding virtual functions below provided in the SBasePlugin class:

  • reading elements :

    1. virtual SBase createObject (XMLInputStream stream)

      This function must be overridden if one or more additional elements are defined.

    2. virtual bool readOtherXML (SBase parentObject, XMLInputStream stream)

      This function should be overridden if elements of annotation, notes, MathML, etc. need to be directly parsed from the given XMLInputStream object.

  • reading attributes (must be overridden if additional attributes are defined) :

    1. virtual void addExpectedAttributes(ExpectedAttributes& attributes)
    2. virtual void readAttributes (XMLAttributes attributes, ExpectedAttributes& expectedAttributes)
  • writing elements (must be overridden if additional elements are defined) :

    1. virtual void writeElements (XMLOutputStream stream)
  • writing attributes :

    1. virtual void writeAttributes (XMLOutputStream stream)

      This function must be overridden if one or more additional attributes are defined.

    2. virtual void writeXMLNS (XMLOutputStream stream)

      This function must be overridden if one or more additional xmlns attributes are defined.

  • checking elements (should be overridden) :

    1. virtual bool hasRequiredElements()

  • checking attributes (should be overridden) :

    1. virtual bool hasRequiredAttributes()

To implement package-specific creating/getting/manipulating functions of the SBasePlugin derived class (e.g., getListOfLayouts(), createLyout(), getLayout(), and etc are implemented in LayoutModelPlugin class of the layout package), package developers must newly implement such functions (as they like) in the derived class.

SBasePlugin class defines other virtual functions of internal implementations such as:

  • virtual void setSBMLDocument(SBMLDocument d)
  • virtual void connectToParent(SBasesbase)
  • virtual void enablePackageInternal(string pkgURI, string pkgPrefix, bool flag)

These functions must be overridden by subclasses in which one or more top-level elements are defined.

For example, the following three SBasePlugin extended classes are implemented in the layout extension:

  1. SBMLDocumentPlugin class for SBMLDocument element

    (SBMLDocumentPlugin class is a common SBasePlugin extended class for SBMLDocument class. Package developers can use this class as-is if no additional elements/attributes (except for required attribute) is needed for the SBMLDocument class in their packages, otherwise package developers must implement a new SBMLDocumentPlugin derived class.)

  2. LayoutModelPlugin class for Model element

    • <listOfLayouts> element is added to Model object.

    • The following virtual functions for reading/writing/checking are overridden: (type of arguments and return values are omitted)

      • createObject() : (read elements)
      • readOtherXML() : (read elements in annotation of SBML L2)
      • writeElements() : (write elements)

    • The following virtual functions of internal implementations are overridden: (type of arguments and return values are omitted)

      • setSBMLDocument()
      • connectToParent()
      • enablePackageInternal()

    • The following creating/getting/manipulating functions are newly implemented: (type of arguments and return values are omitted)

      • getListOfLayouts()
      • getLayout ()
      • addLayout()
      • createLayout()
      • removeLayout()
      • getNumLayouts()

  3. LayoutSpeciesReferencePlugin class for SpeciesReference element (used only for SBML L2V1)

    • id attribute is internally added to SpeciesReference object only for SBML L2V1

    • The following virtual functions for reading/writing/checking are overridden: (type of arguments and return values are omitted)

      • readOtherXML()
      • writeAttributes()

Python method signature(s):

getElementNamespace(SBasePlugin self)   string

Returns the XML namespace (URI) of the package extension of this plugin object.

Returns
the URI of the package extension of this plugin object.
def libsbml.FbcModelPlugin.getFluxBound (   self,
  args 
)

Python method signature(s):

getFluxBound(FbcModelPlugin self, long n)   FluxBound
getFluxBound(FbcModelPlugin self, long n)   FluxBound
getFluxBound(FbcModelPlugin self, string sid)   FluxBound
getFluxBound(FbcModelPlugin self, string sid)   FluxBound

This method has multiple variants that differ in the arguments they accept. Each is described separately below.


Method variant with the following signature:
getFluxBound(long n)

Returns the FluxBound object that belongs to the given index. If the index is invalid, None is returned.

Parameters
nthe index number of the FluxBound to get.
Returns
the nth FluxBound in the ListOfFluxBounds.

Method variant with the following signature:
getFluxBound(string sid)

Returns the FluxBound object based on its identifier.

Parameters
sida string representing the identifier of the FluxBound to get.
Returns
FluxBound in the ListOfFluxBounds with the given sid or None if no such FluxBound exists.
See also
getFluxBound()
getListOfFluxBounds()
def libsbml.FbcModelPlugin.getFluxBoundsForReaction (   self,
  args 
)

Python method signature(s):

getFluxBoundsForReaction(FbcModelPlugin self, string reaction)   ListOfFluxBounds
 
def libsbml.FbcModelPlugin.getGeneAssociation (   self,
  args 
)

Python method signature(s):

getGeneAssociation(FbcModelPlugin self, long n)   GeneAssociation
getGeneAssociation(FbcModelPlugin self, long n)   GeneAssociation
getGeneAssociation(FbcModelPlugin self, string sid)   GeneAssociation
getGeneAssociation(FbcModelPlugin self, string sid)   GeneAssociation

This method has multiple variants that differ in the arguments they accept. Each is described separately below.


Method variant with the following signature:
getGeneAssociation(long n)

Returns the GeneAssociation object that belongs to the given index. If the index is invalid, None is returned.

Parameters
nthe index number of the GeneAssociation to get.
Returns
the nth GeneAssociation in the ListOfGeneAssociations.

Method variant with the following signature:
getGeneAssociation(string sid)

Returns the GeneAssociation object based on its identifier.

Parameters
sida string representing the identifier of the GeneAssociation to get.
Returns
GeneAssociation in the ListOfGeneAssociations with the given sid or None if no such GeneAssociation exists.
See also
getGeneAssociation()
getListOfGeneAssociations()
def libsbml.SBasePlugin.getLevel (   self)
inherited

Python method signature(s):

getLevel(SBasePlugin self)   long

Returns the SBML level of the package extension of this plugin object.

Returns
the SBML level of the package extension of this plugin object.
def libsbml.SBasePlugin.getListOfAllElements (   self,
  filter = None 
)
inherited

Python method signature(s):

getListOfAllElements(SBasePlugin self, ElementFilter filter=None)   SBaseList
getListOfAllElements(SBasePlugin self)   SBaseList

Returns an SBaseList of all child SBase objects, including those nested to an arbitrary depth.

Returns
an SBaseList
def libsbml.FbcModelPlugin.getListOfFluxBounds (   self,
  args 
)

Python method signature(s):

getListOfFluxBounds(FbcModelPlugin self)   ListOfFluxBounds
getListOfFluxBounds(FbcModelPlugin self)   ListOfFluxBounds

Returns the ListOfFluxBounds in this plugin object.

Returns
ListOfFluxBounds object in this plugin object.
def libsbml.FbcModelPlugin.getListOfGeneAssociations (   self,
  args 
)

Python method signature(s):

getListOfGeneAssociations(FbcModelPlugin self)   ListOfGeneAssociations
getListOfGeneAssociations(FbcModelPlugin self)   ListOfGeneAssociations

Returns the ListOfObjectives in this plugin object.

Returns
ListOfObjectives object in this plugin object.
def libsbml.FbcModelPlugin.getListOfObjectives (   self,
  args 
)

Python method signature(s):

getListOfObjectives(FbcModelPlugin self)   ListOfObjectives
getListOfObjectives(FbcModelPlugin self)   ListOfObjectives

Returns the ListOfObjectives in this plugin object.

Returns
ListOfObjectives object in this plugin object.
def libsbml.FbcModelPlugin.getNumFluxBounds (   self)

Python method signature(s):

getNumFluxBounds(FbcModelPlugin self)   long

Returns the number of FluxBound object in this plugin object.

Returns
the number of FluxBound object in this plugin object.
def libsbml.FbcModelPlugin.getNumGeneAssociations (   self)

Python method signature(s):

getNumGeneAssociations(FbcModelPlugin self)   int

Returns the number of GeneAssociation object in this plugin object.

Returns
the number of GeneAssociation object in this plugin object.
def libsbml.FbcModelPlugin.getNumObjectives (   self)

Python method signature(s):

getNumObjectives(FbcModelPlugin self)   long

Returns the number of Objective object in this plugin object.

Returns
the number of Objective object in this plugin object.
def libsbml.FbcModelPlugin.getObjective (   self,
  args 
)

Python method signature(s):

getObjective(FbcModelPlugin self, long n)   Objective
getObjective(FbcModelPlugin self, long n)   Objective
getObjective(FbcModelPlugin self, string sid)   Objective
getObjective(FbcModelPlugin self, string sid)   Objective

This method has multiple variants that differ in the arguments they accept. Each is described separately below.


Method variant with the following signature:
getObjective(long n)

Returns the Objective object that belongs to the given index. If the index is invalid, None is returned.

Parameters
nthe index number of the Objective to get.
Returns
the nth Objective in the ListOfObjectives.

Method variant with the following signature:
getObjective(string sid)

Returns the Objective object based on its identifier.

Parameters
sida string representing the identifier of the Objective to get.
Returns
Objective in the ListOfObjectives with the given sid or None if no such Objective exists.
See also
getObjective()
getListOfObjectives()
def libsbml.SBasePlugin.getPackageName (   self)
inherited

Python method signature(s):

getPackageName(SBasePlugin self)   string

Returns the package name of this plugin object.

Returns
the package name of this plugin object.
def libsbml.SBasePlugin.getPackageVersion (   self)
inherited

Python method signature(s):

getPackageVersion(SBasePlugin self)   long

Returns the package version of the package extension of this plugin object.

Returns
the package version of the package extension of this plugin object.
def libsbml.SBasePlugin.getParentSBMLObject (   self,
  args 
)
inherited

Python method signature(s):

getParentSBMLObject(SBasePlugin self)   SBase
getParentSBMLObject(SBasePlugin self)   SBase

Returns the parent SBase object to which this plugin object connected.

Returns
the parent SBase object to which this plugin object connected.
def libsbml.SBasePlugin.getPrefix (   self)
inherited

Python method signature(s):

getPrefix(SBasePlugin self)   string

Returns the prefix of the package extension of this plugin object.

Returns
the prefix of the package extension of this plugin object.
def libsbml.SBasePlugin.getSBMLDocument (   self,
  args 
)
inherited

Python method signature(s):

getSBMLDocument(SBasePlugin self)   SBMLDocument
getSBMLDocument(SBasePlugin self)   SBMLDocument

Returns the parent SBMLDocument of this plugin object.

Returns
the parent SBMLDocument object of this plugin object.
def libsbml.SBasePlugin.getURI (   self)
inherited

Python method signature(s):

getURI(SBasePlugin self)   string

Gets the URI to which this element belongs to. For example, all elements that belong to SBML Level 3 Version 1 Core must would have the URI 'http://www.sbml.org/sbml/level3/version1/core'; all elements that belong to Layout Extension Version 1 for SBML Level 3 Version 1 Core must would have the URI 'http://www.sbml.org/sbml/level3/version1/layout/version1/'

Unlike getElementNamespace, this function first returns the URI for this element by looking into the SBMLNamespaces object of the document with the its package name. if not found it will return the result of getElementNamespace

Returns
the URI this elements
See also
getPackageName()
getElementNamespace()
SBMLDocument.getSBMLNamespaces()
getSBMLDocument()
def libsbml.SBasePlugin.getVersion (   self)
inherited

Python method signature(s):

getVersion(SBasePlugin self)   long

Returns the SBML version of the package extension of this plugin object.

Returns
the SBML version of the package extension of this plugin object.
def libsbml.FbcModelPlugin.removeFluxBound (   self,
  args 
)

Python method signature(s):

removeFluxBound(FbcModelPlugin self, long n)   FluxBound
removeFluxBound(FbcModelPlugin self, string sid)   FluxBound

This method has multiple variants that differ in the arguments they accept. Each is described separately below.


Method variant with the following signature:
removeFluxBound(long n)

Removes the nth FluxBound object from this plugin object and returns a pointer to it.

The caller owns the returned object and is responsible for deleting it.

Parameters
nthe index of the FluxBound object to remove
Returns
the FluxBound object removed. As mentioned above, the caller owns the returned object. None is returned if the given index is out of range.

Method variant with the following signature:
removeFluxBound(string sid)

Removes the FluxBound object with the given sid attribute from this plugin object and returns a pointer to it.

The caller owns the returned object and is responsible for deleting it.

Parameters
sidthe id attribute of the FluxBound object to remove
Returns
the FluxBound object removed. As mentioned above, the caller owns the returned object. None is returned if the given index is out of range.
def libsbml.FbcModelPlugin.removeGeneAssociation (   self,
  args 
)

Python method signature(s):

removeGeneAssociation(FbcModelPlugin self, long n)   GeneAssociation
removeGeneAssociation(FbcModelPlugin self, string sid)   GeneAssociation

This method has multiple variants that differ in the arguments they accept. Each is described separately below.


Method variant with the following signature:
removeGeneAssociation(long n)

Removes the nth GeneAssociation object from this plugin object and returns a pointer to it.

The caller owns the returned object and is responsible for deleting it.

Parameters
nthe index of the GeneAssociation object to remove
Returns
the GeneAssociation object removed. As mentioned above, the caller owns the returned object. None is returned if the given index is out of range.

Method variant with the following signature:
removeGeneAssociation(string sid)

Removes the GeneAssociation object with the given sid attribute from this plugin object and returns a pointer to it.

The caller owns the returned object and is responsible for deleting it.

Parameters
sidthe id attribute of the GeneAssociation object to remove
Returns
the GeneAssociation object removed. As mentioned above, the caller owns the returned object. None is returned if the given index is out of range.
def libsbml.FbcModelPlugin.removeObjective (   self,
  args 
)

Python method signature(s):

removeObjective(FbcModelPlugin self, long n)   Objective
removeObjective(FbcModelPlugin self, string sid)   Objective

This method has multiple variants that differ in the arguments they accept. Each is described separately below.


Method variant with the following signature:
removeObjective(long n)

Removes the nth Objective object from this plugin object and returns a pointer to it.

The caller owns the returned object and is responsible for deleting it.

Parameters
nthe index of the Objective object to remove
Returns
the Objective object removed. As mentioned above, the caller owns the returned object. None is returned if the given index is out of range.

Method variant with the following signature:
removeObjective(string sid)

Removes the Objective object with the given sid attribute from this plugin object and returns a pointer to it.

The caller owns the returned object and is responsible for deleting it.

Parameters
sidthe id attribute of the Objective object to remove
Returns
the Objective object removed. As mentioned above, the caller owns the returned object. None is returned if the given index is out of range.
def libsbml.FbcModelPlugin.setActiveObjectiveId (   self,
  args 
)

Python method signature(s):

setActiveObjectiveId(FbcModelPlugin self, string objectiveId)   int

Sets the id of the active objective.

def libsbml.SBasePlugin.setElementNamespace (   self,
  args 
)
inherited

Python method signature(s):

setElementNamespace(SBasePlugin self, string uri)   int

Sets the XML namespace to which this element belongs to. For example, all elements that belong to SBML Level 3 Version 1 Core must set the namespace to 'http://www.sbml.org/sbml/level3/version1/core'; all elements that belong to Layout Extension Version 1 for SBML Level 3 Version 1 Core must set the namespace to 'http://www.sbml.org/sbml/level3/version1/layout/version1/'

Returns
integer value indicating success/failure of the function. The possible values returned by this function are:
def libsbml.FbcModelPlugin.unsetActiveObjectiveId (   self)

Python method signature(s):

unsetActiveObjectiveId(FbcModelPlugin self)

Unsets the active objective.